Centromeres of Cucumis melo L. comprise Cmcent and two novel repeats, CmSat162 and CmSat189

Setiawan, Agus Budi; Teo, Chee How; Kikuchi, Shinichi; Sassa, Hidenori; Kato, Kenji; Koba, Takato

doi:10.1371/journal.pone.0227578

Cited by 12 publications

(13 citation statements)

References 39 publications

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“…4). This result suggests that melon centromeres consist of a centromere-specific non-LTR retrotransposon besides centromeric repetitive sequences, CmSat162, CmSat189, and Cmcent [Koo et al, 2010;Setiawan et al, 2020]. Moreover, Menolird18 did not share the sequence homology with these centromeric satellite DNAs of melon (online suppl.…”

Section: Discussionmentioning

confidence: 97%

“…Genomic DNA and Total RNA Isolation Genomic DNA and total RNA were extracted from leaves using the method described by Setiawan et al [2020]. Total RNA was treated with Deoxyribonuclease RT Grade (Nippon Gene, Japan) per themanufacturer's instruction to remove genomic DNA.…”

Section: Data Mining Of Non-ltr Retrotransposonmentioning

confidence: 99%

“…While various types of tandemly organized repetitive DNA sequences in the centromeric regions of melon and their secondary constrictions have been the subject of past research [Koo et al, 2010;Zhang et al, 2016;Setiawan et al, 2018aSetiawan et al, , 2020, dispersed repetitive DNA locations in melon have not been examined. Our study identifies the species-specific chromosomal distribution of a melon (C. melo) and cucumber (C. sativus) LINE (Meno-lird18) and discusses its contribution to the evolution of these Cucumis species.…”

Section: Introductionmentioning

confidence: 99%

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Chromosomal Locations of a Non-LTR Retrotransposon, Menolird18, in Cucumis melo and Cucumis sativus, and Its Implication on Genome Evolution of Cucumis Species

Setiawan

Teo

Kikuchi

et al. 2020

Cytogenet Genome Res

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Mobile elements are major regulators of genome evolution through their effects on genome size and chromosome structure in higher organisms. Non-long terminal repeat (non-LTR) retrotransposons, one of the subclasses of transposons, are specifically inserted into repetitive DNA sequences. While studies on the insertion of non-LTR retrotransposons into ribosomal RNA genes and other repetitive DNA sequences have been reported in the animal kingdom, studies in the plant kingdom are limited. Here, using FISH, we confirmed that Menolird18, a member of LINE (long interspersed nuclear element) in non-LTR retrotransposons and found in Cucumis melo, was inserted into ITS and ETS (internal and external transcribed spacers) regions of 18S rDNA in melon and cucumber. Beside the 18S rDNA regions, Menolird18 was also detected in all centromeric regions of melon, while it was located at pericentromeric and sub-telomeric regions in cucumber. The fact that FISH signals of Menolird18 were found in centromeric and rDNA regions of mitotic chromosomes suggests that Menolird18 is a rDNA and centromere-specific non-LTR retrotransposon in melon. Our findings are the first report on a non-LTR retrotransposon that is highly conserved in 2 different plant species, melon and cucumber. The clear distinction of chromosomal localization of Menolird18 in melon and cucumber implies that it might have been involved in the evolutionary processes of the melon (C. melo) and cucumber (C. sativus) genomes.

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Section: Discussionmentioning

confidence: 97%

Section: Data Mining Of Non-ltr Retrotransposonmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Chromosomal Locations of a Non-LTR Retrotransposon, Menolird18, in Cucumis melo and Cucumis sativus, and Its Implication on Genome Evolution of Cucumis Species

Setiawan

Teo

Kikuchi

et al. 2020

Cytogenet Genome Res

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“…Transcription of CENH3 associated chromatin including centromeric retrotransposons and tandem repeats is now recognized as an important feature for centromere initiation and kinetochore assembly (Topp et al, 2004;Talbert and Henikoff, 2018;Liu et al, 2020;Talbert and Henikoff, 2020). Transcription of CTRs have been observed in a number of plant species including Cucumis melo (Setiawan et al, 2020) and Arabidopsis. We performed bioinformatic and RT-PCR analysis of AcCen1K and AfCen1K expression to detect RNA transcripts from these repeats.…”

Section: Discussionmentioning

confidence: 99%

Functional Allium fistulosum Centromeres Comprise Arrays of a Long Satellite Repeat, Insertions of Retrotransposons and Chloroplast DNA

et al. 2020

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The centromere is a unique part of the chromosome combining a conserved function with an extreme variability in its DNA sequence. Most of our knowledge about the functional centromere organization is obtained from species with small and medium genome/chromosome sizes while the progress in plants with big genomes and large chromosomes is lagging behind. Here, we studied the genomic organization of the functional centromere in Allium fistulosum and A. cepa, both species with a large genome (13 Gb and 16 Gb/1C, 2n = 2x = 16) and large-sized chromosomes. Using low-depth DNA sequencing for these two species and previously obtained CENH3 immunoprecipitation data we identified two long (1.2 Kb) and high-copy repeats, AfCen1K and AcCen1K. FISH experiments showed that AfCen1K is located in all centromeres of A. fistulosum chromosomes while no AcCen1K FISH signals were identified on A. cepa chromosomes. Our molecular cytogenetic and bioinformatics survey demonstrated that these repeats are partially similar but differ in chromosomal location, sequence structure and genomic organization. In addition, we could conclude that the repeats are transcribed and their RNAs are not polyadenylated. We also observed that these repeats are associated with insertions of retrotransposons and plastidic DNA and the landscape of A. cepa and A. fistulosum centromeric regions possess insertions of plastidic DNA. Finally, we carried out detailed comparative satellitome analysis of A. cepa and A. fistulosum genomes and identified a new chromosome-and A. cepa-specific tandem repeat, TR2CL137, located in the centromeric region. Our results shed light on the Allium centromere organization and provide unique data for future application in Allium genome annotation.

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“…This class of repeats is preferentially associated with specific chromosomal segments, most frequently found at centromeric, pericentromeric, and subtelomeric regions but also at intercalary positions [ 4 , 5 , 8 ]. Chromosomal sites rich in satellite DNA usually exhibit a unique banding pattern, which makes them ideal as cytogenetic markers for the identification of individual chromosomes; therefore they are useful for karyotype descriptions [ 9 – 14 ]. FISH with satellite DNA-based probes has also been successfully applied for the understanding of chromosomal evolution in several agronomically important plant species, including sugar beet [ 8 ], maize [ 15 ], radish [ 16 ], common bean [ 17 ], spinach [ 18 ], and quinoa [ 19 ].…”

Section: Introductionmentioning

confidence: 99%

Using carrot centromeric repeats to study karyotype relationships in the genus Daucus (Apiaceae)

Kadluczka

Grzebelus

2021

BMC Genomics

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Background In the course of evolution, chromosomes undergo evolutionary changes; thus, karyotypes may differ considerably among groups of organisms, even within closely related taxa. The genus Daucus seems to be a promising model for exploring the dynamics of karyotype evolution. It comprises some 40 wild species and the cultivated carrot, a crop of great economic significance. However, Daucus species are very diverse morphologically and genetically, and despite extensive research, the taxonomic and phylogenetic relationships between them have still not been fully resolved. Although several molecular cytogenetic studies have been conducted to investigate the chromosomal structure and karyotype evolution of carrot and other Daucus species, detailed karyomorphological research has been limited to carrot and only a few wild species. Therefore, to better understand the karyotype relationships within Daucus, we (1) explored the chromosomal distribution of carrot centromeric repeats (CentDc) in 34 accessions of Daucus and related species by means of fluorescence in situ hybridization (FISH) and (2) performed detailed karyomorphological analysis in 16 of them. Results We determined the genomic organization of CentDc in 26 accessions of Daucus (belonging to both Daucus I and II subclades) and one accession of closely related species. The CentDc repeats were present in the centromeric regions of all chromosomes of 20 accessions (representing 11 taxa). In the other Daucus taxa, the number of chromosome pairs with CentDc signals varied depending on the species, yet their centromeric localization was conserved. In addition, precise chromosome measurements performed in 16 accessions showed the inter- and intraspecific karyological relationships among them. Conclusions The presence of the CentDc repeats in the genomes of taxa belonging to both Daucus subclades and one outgroup species indicated the ancestral status of the repeat. The results of our study provide useful information for further evolutionary, cytotaxonomic, and phylogenetic research on the genus Daucus and may contribute to a better understanding of the dynamic evolution of centromeric satellites in plants.

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Centromeres of Cucumis melo L. comprise Cmcent and two novel repeats, CmSat162 and CmSat189

Cited by 12 publications

References 39 publications

Chromosomal Locations of a Non-LTR Retrotransposon, <b><i>Menolird18</i></b>, in <b><i>Cucumis melo</i></b> and <b><i>Cucumis sativus</i></b>, and Its Implication on Genome Evolution of <b><i>Cucumis</i></b> Species

Chromosomal Locations of a Non-LTR Retrotransposon, <b><i>Menolird18</i></b>, in <b><i>Cucumis melo</i></b> and <b><i>Cucumis sativus</i></b>, and Its Implication on Genome Evolution of <b><i>Cucumis</i></b> Species

Functional Allium fistulosum Centromeres Comprise Arrays of a Long Satellite Repeat, Insertions of Retrotransposons and Chloroplast DNA

Using carrot centromeric repeats to study karyotype relationships in the genus Daucus (Apiaceae)

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